Job ID = 14159584 SRX = SRX3180772 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 9472625 spots for SRR6030423/SRR6030423.sra Written 9472625 spots for SRR6030423/SRR6030423.sra fastq に変換しました。 bowtie でマッピング中... Your job 14159859 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:22 9472625 reads; of these: 9472625 (100.00%) were unpaired; of these: 552401 (5.83%) aligned 0 times 7009309 (74.00%) aligned exactly 1 time 1910915 (20.17%) aligned >1 times 94.17% overall alignment rate Time searching: 00:02:22 Overall time: 00:02:22 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 3290769 / 8920224 = 0.3689 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 22:53:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3180772/SRX3180772.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3180772/SRX3180772.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3180772/SRX3180772.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3180772/SRX3180772.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Wed, 08 Dec 2021 22:53:06: #1 read tag files... INFO @ Wed, 08 Dec 2021 22:53:06: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 22:53:13: 1000000 INFO @ Wed, 08 Dec 2021 22:53:21: 2000000 INFO @ Wed, 08 Dec 2021 22:53:28: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 22:53:35: 4000000 INFO @ Wed, 08 Dec 2021 22:53:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3180772/SRX3180772.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3180772/SRX3180772.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3180772/SRX3180772.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3180772/SRX3180772.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Wed, 08 Dec 2021 22:53:36: #1 read tag files... INFO @ Wed, 08 Dec 2021 22:53:36: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 22:53:42: 5000000 INFO @ Wed, 08 Dec 2021 22:53:45: 1000000 INFO @ Wed, 08 Dec 2021 22:53:46: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 22:53:46: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 22:53:46: #1 total tags in treatment: 5629455 INFO @ Wed, 08 Dec 2021 22:53:46: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 22:53:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 22:53:46: #1 tags after filtering in treatment: 5629455 INFO @ Wed, 08 Dec 2021 22:53:46: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 22:53:46: #1 finished! INFO @ Wed, 08 Dec 2021 22:53:46: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 22:53:46: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 22:53:47: #2 number of paired peaks: 675 WARNING @ Wed, 08 Dec 2021 22:53:47: Fewer paired peaks (675) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 675 pairs to build model! INFO @ Wed, 08 Dec 2021 22:53:47: start model_add_line... INFO @ Wed, 08 Dec 2021 22:53:47: start X-correlation... INFO @ Wed, 08 Dec 2021 22:53:47: end of X-cor INFO @ Wed, 08 Dec 2021 22:53:47: #2 finished! INFO @ Wed, 08 Dec 2021 22:53:47: #2 predicted fragment length is 49 bps INFO @ Wed, 08 Dec 2021 22:53:47: #2 alternative fragment length(s) may be 3,49 bps INFO @ Wed, 08 Dec 2021 22:53:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3180772/SRX3180772.05_model.r WARNING @ Wed, 08 Dec 2021 22:53:47: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 22:53:47: #2 You may need to consider one of the other alternative d(s): 3,49 WARNING @ Wed, 08 Dec 2021 22:53:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 22:53:47: #3 Call peaks... INFO @ Wed, 08 Dec 2021 22:53:47: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 22:53:53: 2000000 INFO @ Wed, 08 Dec 2021 22:53:58: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 22:54:00: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 22:54:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3180772/SRX3180772.05_peaks.xls INFO @ Wed, 08 Dec 2021 22:54:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3180772/SRX3180772.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 22:54:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3180772/SRX3180772.05_summits.bed INFO @ Wed, 08 Dec 2021 22:54:04: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (731 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 22:54:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3180772/SRX3180772.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3180772/SRX3180772.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3180772/SRX3180772.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3180772/SRX3180772.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Wed, 08 Dec 2021 22:54:06: #1 read tag files... INFO @ Wed, 08 Dec 2021 22:54:06: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 22:54:08: 4000000 INFO @ Wed, 08 Dec 2021 22:54:13: 1000000 INFO @ Wed, 08 Dec 2021 22:54:16: 5000000 INFO @ Wed, 08 Dec 2021 22:54:20: 2000000 INFO @ Wed, 08 Dec 2021 22:54:21: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 22:54:21: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 22:54:21: #1 total tags in treatment: 5629455 INFO @ Wed, 08 Dec 2021 22:54:21: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 22:54:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 22:54:21: #1 tags after filtering in treatment: 5629455 INFO @ Wed, 08 Dec 2021 22:54:21: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 22:54:21: #1 finished! INFO @ Wed, 08 Dec 2021 22:54:21: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 22:54:21: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 22:54:22: #2 number of paired peaks: 675 WARNING @ Wed, 08 Dec 2021 22:54:22: Fewer paired peaks (675) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 675 pairs to build model! INFO @ Wed, 08 Dec 2021 22:54:22: start model_add_line... INFO @ Wed, 08 Dec 2021 22:54:22: start X-correlation... INFO @ Wed, 08 Dec 2021 22:54:22: end of X-cor INFO @ Wed, 08 Dec 2021 22:54:22: #2 finished! INFO @ Wed, 08 Dec 2021 22:54:22: #2 predicted fragment length is 49 bps INFO @ Wed, 08 Dec 2021 22:54:22: #2 alternative fragment length(s) may be 3,49 bps INFO @ Wed, 08 Dec 2021 22:54:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3180772/SRX3180772.10_model.r WARNING @ Wed, 08 Dec 2021 22:54:22: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 22:54:22: #2 You may need to consider one of the other alternative d(s): 3,49 WARNING @ Wed, 08 Dec 2021 22:54:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 22:54:22: #3 Call peaks... INFO @ Wed, 08 Dec 2021 22:54:22: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 22:54:26: 3000000 INFO @ Wed, 08 Dec 2021 22:54:33: 4000000 INFO @ Wed, 08 Dec 2021 22:54:33: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 22:54:39: 5000000 INFO @ Wed, 08 Dec 2021 22:54:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3180772/SRX3180772.10_peaks.xls INFO @ Wed, 08 Dec 2021 22:54:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3180772/SRX3180772.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 22:54:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3180772/SRX3180772.10_summits.bed INFO @ Wed, 08 Dec 2021 22:54:39: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (543 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 22:54:43: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 22:54:43: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 22:54:43: #1 total tags in treatment: 5629455 INFO @ Wed, 08 Dec 2021 22:54:43: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 22:54:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 22:54:43: #1 tags after filtering in treatment: 5629455 INFO @ Wed, 08 Dec 2021 22:54:43: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 22:54:43: #1 finished! INFO @ Wed, 08 Dec 2021 22:54:43: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 22:54:43: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 22:54:44: #2 number of paired peaks: 675 WARNING @ Wed, 08 Dec 2021 22:54:44: Fewer paired peaks (675) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 675 pairs to build model! INFO @ Wed, 08 Dec 2021 22:54:44: start model_add_line... INFO @ Wed, 08 Dec 2021 22:54:44: start X-correlation... INFO @ Wed, 08 Dec 2021 22:54:44: end of X-cor INFO @ Wed, 08 Dec 2021 22:54:44: #2 finished! INFO @ Wed, 08 Dec 2021 22:54:44: #2 predicted fragment length is 49 bps INFO @ Wed, 08 Dec 2021 22:54:44: #2 alternative fragment length(s) may be 3,49 bps INFO @ Wed, 08 Dec 2021 22:54:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3180772/SRX3180772.20_model.r WARNING @ Wed, 08 Dec 2021 22:54:44: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 22:54:44: #2 You may need to consider one of the other alternative d(s): 3,49 WARNING @ Wed, 08 Dec 2021 22:54:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 22:54:44: #3 Call peaks... INFO @ Wed, 08 Dec 2021 22:54:44: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 22:54:55: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 22:55:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3180772/SRX3180772.20_peaks.xls INFO @ Wed, 08 Dec 2021 22:55:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3180772/SRX3180772.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 22:55:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3180772/SRX3180772.20_summits.bed INFO @ Wed, 08 Dec 2021 22:55:01: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (254 records, 4 fields): 2 millis CompletedMACS2peakCalling